Leaky gut, as you might be imagining it in your head, is layman terminology for intestines that have increased permeability.

This can be due to a variety of reasons, which we’ll dive into shortly, but first let’s provide a basic understanding of how the GI tract works.

The gut is a tube that is about 20-25 feet long, covers 3000 square feet (the size of a tennis court) of surface area and is only one cell layer thick, according to Dr. Mark Hyman.7

There are spaces between this single layer of intestinal cells that open and close to allow only specific, very small molecules to pass. These spaces are controlled by tight junctions.

What Exactly is Leaky Gut or Intestinal Hyper-Permeability?

The primary purpose of the GI tract is to provide barrier function, as well as to allow the selective passage of substances it deems beneficial, all the while keeping foreign invaders out.

Every second of every day, your intestinal cells, along with the immune, neurological and hormonal components within them, screen your environment in an effort to keep you healthy.

Leaky gut occurs when there is a breakdown in this barrier function allowing substances to enter the bloodstream that normally wouldn’t be there, resulting in immune system activation and inflammation.

Dr. Alessio Fasano lays it out nicely, saying that “The intestinal mucosa is the battlefield on which friends and foes need to be recognized and properly managed to find the balance between TOLERANCE and the immune response.”2,3,4

How Does Leaky Gut Occur?

The tight junctions in a healthy gut operate like a club bouncer, selecting what to allow past the “velvet rope” and into the bloodstream. Simply put, they keep bad things out and allow good things through.

In a Leaky Gut however, the tight junctions leave the “velvet rope” unattended, allowing everything to pass through. This can result in serious problems.

Technically speaking, Leaky Gut, also commonly referred to as intestinal hyper-permeability, occurs when inflammation leads to the breakdown of the mechanism that controls the tight junctions between the intestinal cells, allowing them to become looser. This allows the “leaking” of either larger and/or foreign particles through to your bloodstream.

Modern lifestyles place a lot of stress on the gut in the form of poor diet, medications, alcohol, infections and environmental toxins, leading to chronic irritation, inflammation and ultimately the breakdown of the intestinal barrier.

This delicate layer that should be selective and tightly regulated, now has tiny pin-prick like holes in it that allow foreign substances such as undigested foods, bacteria, yeast and toxins to cause an immune response.

As this scenario progresses over time, a variety of conditions can arise, including acne, allergies, asthma, fatigue and joint pain, or even more serious ones such as Hashimoto’s, Graves’ Disease, Psoriasis and other autoimmune conditions.

Triggers of Leaky Gut

The most common triggers of Leaky Gut are:

Stress

Diet

Infections

Toxins

Medications

Trigger: Stress

Stress is a significant trigger and mediator in the development of Leaky Gut. According to Chris Kresser, LAc, “The biochemical changes that occur in times of stress have significant and immediate impact on gut function.”1

Once your body perceives a stressor, whether it’s work, infection, exercise, food or toxin, it mounts a biochemical response that results in increased gut permeability, mediation of inflammation, increased sensitivity to pain, altered gut motility and changes to the gut microflora. Over time this can lead to significant changes in GI function.

Kresser states that “Experimental studies have shown that psychological stress slows normal small intestinal transit time, encourages overgrowth of bacteria, and even compromises the intestinal barrier.”1

These changes provide the gateway for other triggers to wreak havoc, as larger food particles, toxins, and pathogens enter the bloodstream through the gut, and thus the immune response occurs.

Trigger: Diet

While the stresses of work and family are of noteworthy significance, the food that you eat is actually the biggest daily stressor, as perceived by your body, according to Dr. Robert Rountree.5

Common gut-damaging foods include:

Gluten: A protein that has been hybridized (changed from its original form) to the point that your body sees it as foreign and reacts to it.9,10

Sugar and Refined Carbohydrates: Support yeast overgrowth and promote bad bacteria over good bacteria.

Alcohol: Alcohol and its by-products are direct toxins and irritants to the GI mucosa. It’s also linked to yeast and SIBO infections.

Food Sensitivities and Allergies: Gluten, Dairy, Corn, Soy, Yeast, Eggs, and Nuts are the most common offenders. With Leaky Gut, larger food particles enter your blood and the immune system responds. Since you’re likely eating very frequently, the result can be a continuous cycle of inflammation and immune upregulation.

Lectins and Phytates: Nutrient blockers that are produced by plants for survival that cause mineral malabsorption and alter the gut lining leading to immune activation. These are widespread in grains, legumes, and nuts.9,10

Conventional Dairy: The protein A1 Casein damages the gut lining, and according to Dr. Josh Axe, pasteurization causes degradation of enzymes that are critical to digestion of lactose.11

Trigger: Infections

GI infections such as Candida (yeast), parasites, H. pylori, and SIBO (small intestinal bacterial overgrowth) release toxic metabolic products that cause inflammation to the gut lining, as well as the breakdown of its physical barrier.

This toxic process also makes the intestines more hospitable to other pathogens, leaving you vulnerable to additional infections.

The presence of these GI infections also contributes to dysbiosis, or the imbalance of the bad gut flora over the good flora, essentially wiping away another level of defense against invaders and allowing the toxic environment to flourish.

Infections such as Lyme Disease and other tick borne illnesses, as well as certain viruses, can also play a role in the development of Leaky Gut, by contributing to processes that alter normal digestion and elimination, as well as perpetuate inflammation.16

Infections can also further complicate the situation through molecular mimicry.

Molecular mimicry occurs when the body mistakes a self-molecule for a foreign molecule and in error mounts an immune attack on its own tissue.14

A classic example is the bacteria Klebsiella attacking the joints, resulting in Ankylosing Spondylitis.15

Due to molecular mimicry, bacteria and parasites are often found to be root causes in the development of various autoimmune conditions.14, 15

Trigger: Toxins

In addition to the toxins produced from bacteria, yeast, and parasites, your body is exposed to an excessive amount of daily contaminants.

According to the EPA there are over 70,000 chemicals in U.S. commerce today.12 Some common ones include:

Toxins can damage intestinal cells, alter the gut nervous and immune systems, or even kill beneficial bacteria. The worst effect however, may be that these toxins are being reabsorbed and recirculated rather than eliminated from your body.

Even the hormones in your body can act as toxins because they can be re-absorbed into circulation if the flora is imbalanced and the gut is permeable.

Trigger: Medications

Anti-inflammatories, antibiotics and acid blocking drugs are the main medication-type contributors to Leaky Gut.

NSAIDs actually block the production of prostaglandins, which are substances that can mediate pain, but that are also critical to rebuilding the lining of the intestines.

According to Dr. Leo Galland, NSAIDs can further cause damage by sensitizing bacteria and altering the GI flora.13 He states, “If you use a full therapeutic dose of NSAIDs for 2 weeks there is a 75% chance you will develop a leaky gut that will not go away when you stop taking the drug.”13

Along with killing pathogens, antibiotics also kill the good bacteria, creating the potential for yeast overgrowth, which directly causes and perpetuates Leaky Gut.

Acid blockers decrease the amount of stomach acid produced. This results in suppressed and incomplete digestion of food, which allows large particles through the intestines and into the bloodstream. This increases the likelihood of immune system reaction. Further, decreased stomach acid leaves you vulnerable to pathogens, as there isn’t enough acid to kill them.

If you’re experiencing symptoms that lead you to suspect Leaky Gut, you should address them quickly.

According to Dr. Tom Sult, “As the condition of the gut degrades, the health implications can become serious.”6

Minor Symptoms tend to be largely limited to the gut early on in the condition, where as a more progressive case will have symptoms outside of the gut.6

The more symptoms that you have, the higher the correlation to an increased immune system response and the subsequent possibility to develop more serious conditions that can be difficult to reverse, such as autoimmune conditions.

Every single autoimmune condition is thought to have the same root cause: Leaky Gut. Dr. Alessio Fasano’s research has been integral in identifying this linkage. In his 2012 paper titled “Leaky Gut and Autoimmune Disease,” he states, “In addition to the genetic predisposition and exposure to triggering non-self antigens, the loss of protective function of the mucosal barriers that interact with the environment (mainly through the GI and lung mucosa) is necessary for autoimmunity to develop.”2,4

Dr. Leo Galland explains that even though you have a leaky gut, the cells of the intestinal lining replace themselves every 3-6 days.13

This means that once you eliminate the contributing triggers and root causes of Leaky Gut you can repair the intestines fairly quickly. The hard part can be identifying all of the causes and eliminating them.

Functional Medicine’s approach to the treatment of Leaky Gut is the 5R Program:

Remove the sources of irritation and inflammation:

Eliminate foods that contribute to leaky gut. Completing an elimination diet for 3-4 weeks is a good place to start.

Using a food diary is a great tool to identify food sensitivities when you add them back in. If you add them back in and have any type of reaction, you should keep them out until your gut is fully healed.

Try to eliminate the use of medications known to contribute to leaky gut, if you can.

Reduce toxin exposure by eating organic when possible, using cleaner personal care and home products, and filtering your home air and water. Many green plants provide natural toxin filtration.

Remove all sources of parasitic, fungal, and bacterial infections in the gut. If you take care of these without resolution of symptoms, look into viruses and other infections such as tick borne illnesses.

Replace the nutrients that your body needs to heal:

Using digestive enzymes and betaine hydrochloride to allow for proper breakdown and absorption of nutrients.

Taking a good multivitamin can help restore nutrients while your body is still not completely digesting and absorbing food.

Glutamine is an amino acid that is the primary source of fuel for intestinal cells. Supplementing with glutamine at 5-10g twice daily can help heal the gut lining faster.

Omega-3 fatty acids found in fish oils can help decrease inflammation taken at a dose of 2-4 g per day.

Supplements that contain Slippery Elm, Marshmallow Root, Aloe, DGL, and Zinc Carnosine are soothing to the gut mucosa. Use these cautiously as some of them can cause GI distress in people with certain dietary restrictions and autoimmune conditions.15

Reinoculate with good bacteria to restore the flora:

Using a high quality probiotic with at least 50 billion CFU twice daily will help restore the gut flora. Lactobacillus and Bifidobacter species are best.

Fermented foods such as sauerkraut, kimchi and kombucha, as well as kefir and yogurt (you can use dairy or non-dairy based) contain live, active cultures that will help the good bacteria stick around.

Prebiotic fibers and resistant starches provide the nutrients that support the healthy flora and maintain intestinal health.

Repair the gut lining and normal physiological functions.

Taking many of the supplements described in #2 and #3 will help repair and rebuild the gut lining.

In addition, it’s important to also repair the normal physiological processes of digestion, or you risk developing a leaky gut again. This includes using betaine HCl to increase stomach acid, digestive enzymes to assist the pancreas, intestines and liver until they produce adequate levels on their own, and sometimes ox bile to assist the liver in the digestion of fats.

Additionally, motility, or the ability to keep waste and toxins moving through the GI tract, often needs to be repaired and restored.

Ginger and d-limonene are good agents to stimulate GI motility. Exercise and movement are also great ways to keep the bowels moving.

Nothing says good morning quite like pooping into a toilet hat and transferring part of that specimen, using a spoon, into a test tube. While this might sound a little gross on the surface, it can tell you a lot about your health.

The condition of your gut and how well you can absorb, utilize, and eliminate nutrients represents the foundation of health in your body. Digestive symptoms manifest as anything from brain fog, fatigue and acne, to diarrhea, gas, and bloating. The symptoms are vast and can be confusing, so clearly knowing what you’re looking for helps.

Symptoms of Digestive Problems

Understanding your symptoms can be a useful guide for choosing the correct test.

Choosing digestive tests can be a daunting task, especially when the symptoms seem to be coming from everywhere in your body. Starting off with the basics and expanding from there is always a good way to proceed when doing any testing.

The first thing to consider is if the symptoms suggest an acute infection, such as parasites or food poisoning. If this is the case, then testing to identify the organism is best. This usually involves a stool test and/or blood testing.

If your symptoms are chronic or more vague, then approaching tests with a broader scope can more easily pinpoint the root causes (there are often many). Dysbiosis, malabsorption, nutrient depletion, and GI dysfunctions like increased or decreased transit time often occur together.

When using this approach, the first goal is to identify and eliminate all pathogens, because if they’re present, you’ll have dysbiosis. Next, identifying the composition of the gut flora and checking immune and gut function will help direct treatment in the healing and rebuilding phases.

Occasionally, things don’t go like you want them to and further testing is warranted. Some companies offer specialty tests for food sensitivities or allergies (like celiac), detoxification, specific toxin testing, and hidden infections. We’ll get to these types of tests later on.

Digestive Testing

General tests can be completed by lab companies such as LabCorp or Quest, as well as specialty labs:

Functional tests are more in-depth than standard digestive tests. They’re provided by specialty labs and often require a practitioner to request them for you:

Organic acids dysbiosis profile

Comprehensive digestive stool analysis (CDSA)

Intestinal permeability

Lactose intolerance breath testing

SIBO (small intestinal bacterial overgrowth) breath testing

Stool Testing

Stool testing is just what it sounds like—an examination of your stool for good and bad organisms, toxins, and the presence of blood.

Typically, stool tests incorporate a stool culture of common bacteria, microscopic analysis for yeast, fungi, parasites, and blood cells, and sometimes testing for toxins that organisms excrete, such as the Shiga toxins (E. coli) or Clostridium difficile toxins A and B.

Additionally, most of the functional/specialty labs do antibody tests for hard-to-identify organisms, such as Giardia lamblia, Cryptosporidium parvum, Entamoeba histolytica, and Helicobacter pylori as a part of their normal stool testing.

One of the big differences is that some labs offer one-day tests while others offer three-day tests. The benefit to three days’ worth of samples is that there’s a greater chance of identifying elusive GI organisms.

That’s not the whole story, though. While most labs rely on traditional methods to identify organisms, some labs offer PCR-based testing, which means they’re using DNA to identify and only require one sample.

Serum testing requires a blood draw, and the sample will be used to identify any organisms in your bloodstream. This may happen if you’ve had a systemic illness that may have spread from another area, such as the digestive or urinary tracts.

Bacteria, yeast, and other fungi are often identified in this manner. Yeast is especially important to consider here, because it’s opportunistic and will go beyond the limits of the GI tract in people with compromised immune function or co-infections.

This test is most likely to be conducted through a standard lab, at a hospital, or through your doctor’s office. It’s not something offered through specialty labs.

Antibody or Antigen Testing for Infections

Antibody testing is similar to serum testing in that it offers another means of identifying sometimes hard-to-locate organisms. Antibody testing can be done on blood or stool. When you have an infection, your body mounts an immune attack and creates antibodies against that specific organism’s antigen (the protein your body identifies as foreign).

Antibody tests measure your body’s immune response to an organism. This type of testing lets you know that there was an organism present at some moment in time, but it won’t necessarily tell you if it’s active, since antibodies can remain elevated even after the intruder is eliminated.

Similarly, antigen testing can identify the presence of an organism. Performing a stool antigen test for H. pylori is a preferred method, as it’s less invasive than other methods and is both sensitive and specific for active infection.

Antibody and antigen testing can be run through standard labs, as well as via BioHealth Laboratory, Genova Diagnostics, Doctor’s Data, and DRG Laboratory.

Organic Acids Dysbiosis Profile

Urinary organic acids measure the byproducts of your metabolic processes. Specifically, it’s measuring the metabolites produced by the bacteria and yeast living in your gut. This is a simple and non-invasive test, since it requires only a urine sample.

Intestinal bacterial overgrowth and yeast infections will cause elevated metabolites, and they’re also useful in assessing carbohydrate and protein malabsorption.

Urinary organic acid testing is available through Great Plains Laboratories and Genova Diagnostics.

Comprehensive Digestive Stool Analysis (CDSA)

Comprehensive digestive stool analysis is another way to evaluate the health of the GI tract. Using microbial growth-based cultures, biochemical assays, and microscopic evaluation, this thorough test assesses the status of beneficial and pathogenic microorganisms, including aerobic and anaerobic bacteria, yeast, and parasites. Specific analysis includes:

Identification of pathogenic bacteria, parasites, and fungi, and levels of beneficial bacteria

Protein, carbohydrate, and fat absorption via elastase and chymotrypsin levels, as well as the presence of meat and vegetable fibers and fats

Many of these markers can also be tested as smaller profiles or individual tests. The full test is offered by Genova Diagnostics and Doctor’s Data, while DRG Laboratories can do a pared-down version with their stool PCR testing.

Intestinal Permeability Testing

This test provides a method for verifying the presence of increased intestinal permeability, also called leaky gut. Leaky gut allows food particles, toxins, and products of dysbiosis to enter the bloodstream, where an immune response mounts and inflammation is produced. It’s implicated in many conditions, from IBS to autoimmunity.

One version of the test, the Lactulose-Mannitol test, requires you to drink a solution of the sugars lactulose and mannitol. The degree of permeability is assessed by the amount of sugar recovered in urine.

An updated version of permeability testing called Intestinal Antigenic Permeability Screening assesses IgA, IgM, and IgG antibody reactions to bacterial endotoxins (LPS) that have entered the bloodstream. It also measures the tight junction proteins zonulin and occludin that break down in leaky gut, as well as a cell structure component called actomyosin. This test may more specifically show the route of gut barrier damage.

Lactose intolerance is one of the most common food intolerances in the US. Consumption of dairy that causes gas, bloating, diarrhea, and abdominal pain is an indication for this type of test. Inability to break down the dairy sugar lactose because of a lack of the digestive enzyme lactase or intestinal irritation results in lactose malabsorption and digestive symptoms.

This test requires you to drink a lactose solution and then take breath samples over a period of several hours. It measures the amount of hydrogen and methane produced when undigested and absorbed lactose is fermented by gut bacteria.

Genova Diagnostics offers this test.

SIBO Breath Testing

Small intestinal bacterial overgrowth (SIBO) occurs when large amounts of bacteria are present in the small intestine, where there are normally very few. The small intestine is where absorption largely takes place, so there’s little need of bacteria.

The symptoms are similar to lactose intolerance, because the bacteria are fermenting undigested foods (especially carbohydrates) and producing methane or hydrogen. Bloating, gas, abdominal pain, diarrhea, and constipation are classic symptoms.

During this test, you consume solution of glucose or lactulose, and then breath samples are taken over a period of 2-3 hours. The test measures the amount of hydrogen and methane produced when undigested and unabsorbed lactose is fermented by gut bacteria. High methane is associated with constipation, and high hydrogen levels correlate with diarrhea.

Genova Diagnostic and Commonwealth Labs both offer this test.

Summary

There’s certainly no shortage of digestive testing for you to explore. If you don’t get answers from basic tests, perhaps it could be time to consider more functional testing. Many of the tests referenced above can be ordered through Direct Labs, and can shed much light on the root causes of your health symptoms- and like G.I. Joe used to say, knowing is half the battle.

Most of us have felt that special feeling. You know the one. Great night out with friends, maybe even a special someone. And then the next morning rolls around. THAT feeling.

You wake up to a pounding head, nausea, aches, brain fog and an inability to focus. That’s your liver screaming at you.

Those extra few drinks just needed to happen, huh?

So those are obvious signs that we recognize easily, but did you know that when your hormones are out of whack, your blood sugar is erratic, and you constantly feel sluggish, your liver is STILL speaking to you?

Most of us are great at listening to our bodies when we experience something as uncomfortable and excruciating as a bad hangover, but we’re more likely to ignore the signs when they’re less obvious or when they require lifestyle changes that we may not want to make.

The liver is the largest internal organ and has extraordinary resiliency, as it’s bombarded daily with an onslaught of assaults from air pollution, environmental toxins, medications, and microorganisms (bacteria, mold, fungi, and viruses).

It’s clear that it takes a lot to knock the liver down, but somehow, in our crazy, high-stress lives, we find a way to do just that.

Impaired detoxification and liver function is the predecessor of many systemic diseases, including liver disease. At least 30 million people, or 1 in 10 Americans, has some type of liver disease.1

If you consider some of the other conditions where liver function is important, including autoimmunity, cancer, cardiovascular disease, diabetes, and high cholesterol, it’s obvious that proper liver function and detoxification are central to health. So it’s important that we recognize the signs of impaired detoxification before it has the chance to become a full-blown condition, because reversing it is much easier than reversing most chronic diseases.

What Exactly is Liver Detoxification?

Detoxification is the process of transforming and removing harmful substances from the body. Normally, the liver takes a toxic substance, then neutralizes and transforms it so that it can be eliminated in a healthy way that doesn’t damage the body.

Once your liver detoxifies and breaks down a substance, it’s excreted to the blood or bile for elimination. Blood products are filtered through the kidneys and eliminated as urine, while bile products are sent to the intestines and eliminated as feces. Some items are also eliminated through sweat and breathing.

When detoxification doesn’t occur efficiently and properly, the liver becomes taxed and sluggish, which impacts almost every system of the body in some way. The liver plays a role (to varying degrees) in most biological functions, being responsible for over 200 tasks. Here is a short list of some other liver functions that detoxification impacts:2,3

Conversion of harmful ammonia to urea

Clearance of bilirubin (if there’s a buildup of bilirubin, the skin and eyes turn yellow in a condition called jaundice)

Storage of essential vitamins and minerals, and conversion to their biologically active forms

Regulation of amino acid and protein metabolism

Maintenance of hormone balance

Impaired detox results in changes to all of the above processes, which can manifest as imbalanced hormones, high cholesterol, blood sugar abnormalities, decreased immune function, increased inflammation and pain, and a variety of symptoms ranging from fatigue and brain fog to rashes and headaches.

How Does Liver Detoxification Become Impaired?

Impaired liver detoxification occurs when any substance or disease process compromises the liver’s ability to perform its basic metabolic functions.

When your liver can’t function properly, toxins and metabolic waste back up and accumulate in your body, making you feel horrible and causing damage to your cells.

A good way to imagine this is to think about it like taking out the trash. If you empty the waste bins throughout your house daily, even every couple of days, you’re probably in good shape.

But what if you let it pile up for a month, or even a year? Pretty soon you’re looking like you belong on a late-night cable TV show because your house is teeming with bacteria, mold, parasites, and volatile chemicals, soon to be deemed uninhabitable by the health department. When your liver can’t empty the trash on a continual basis, this is what happens inside your body.

Damage to your liver cells can occur through a variety of mechanisms:3

Metabolic disorders such as obesity, diabetes, and fatty liver

A high sugar and carbohydrate diet or processed foods

Illnesses that produce toxins and inflammation or promote malabsorption

Infections such as Candida, viral hepatitis, and any GI infection/dysbiosis

What all of these processes have in common is that they damage liver cells in some form, whether from oxidative stress, inflammation, or a lack of the nutrients the liver needs in order to work properly. The damage results in impaired detoxification systems.

Detoxification processes in the liver are controlled by many genes and the Phase 1, 2, and 3 detoxification pathways. In order for detoxification to occur properly, the genes that control the process need the correct nutrients and environment (epigenetics) to properly regulate the enzymes that control the detoxification pathways.

One group of genes that have received publicity lately are the methylation pathway genes (MTHFR, MTRR, CBS, COMT, etc.), and rightfully so. This group of genes plays a central role in detoxification, as well as neurotransmitter, hormone, and amino acid metabolism, cardiovascular health, DNA synthesis, and gene regulation.

Sometimes there are changes in a gene—SNPs, or single nucleotide polymorphisms—that alter the function of the corresponding enzyme that controls a process such as detoxification.

When you have an SNP, it changes the gene’s instruction manual, which alters the way the enzymes work.

For instance, if you have one copy of an MTHFR (methylene tetrahydrofolate reductase enzyme) gene SNP, you’ll have a 30% reduction in the activity of the enzyme. If you have 2 copies of the SNP, you’ll have a 70% reduction in enzyme activity and significantly impaired detoxification. Many people have multiple SNPs in this pathway, resulting in reduced detoxification capacity.

Similarly, the 60 cytochrome P450 (CYP450) family of enzymes that are primarily found in the liver play a significant role in the breakdown of toxins. SNPs affect the CYP450 enzymes as well—especially those involving drug metabolism.

“Depending on the gene and the polymorphism, drugs and supplements can be metabolized quickly or slowly. If a cytochrome P450 enzyme metabolizes a drug slowly, the drug stays active longer and less is needed to get the desired effect. A drug that’s quickly metabolized is broken down sooner, and a higher dose might be necessary to be effective. Cytochrome P450 enzymes account for 70 to 80 percent of enzymes involved in drug metabolism.”5

The Phase I detoxification system is controlled by these CYP450 enzymes and is the first step toxins go through in the breakdown process. Once toxins enter this pathway, the substance undergoes a chemical transformation, producing an intermediate that’s often as toxic or more toxic than the original substance.

This isn’t a big problem if your Phase 2 detoxification pathways are sufficient, but there can be SNPs here too, reducing the process’ efficiency and causing you systemic problems.

Phase 2 detoxification reactions involve the conjugation (coupling) of the Phase 1 intermediate to a substance, making it water-soluble and suitable for elimination via urine and bile (feces).

Essentially, what’s happening in all of these processes is that the intermediate is combined with a specific type of molecule that neutralizes it for elimination. For example, in methylation, a methyl group (CH3) is transferred to the intermediate. Once this process takes place, the neutralized substance can be eliminated.

Phase 3 of detoxification takes the neutralized substance and transports it out of the liver cell to be excreted in the urine or bile.

Diet, nutritional status, illness, toxic burden, dysbiosis, and SNPs all affect the efficiency of the detox pathways, and vice versa. Identifying any potential roadblocks and cleaning up your personal environment and/or lifestyle is necessary to have detoxification systems running at peak performance.

Triggers of Impaired Liver Detoxification

We have toxins around and inside us that come in many forms. If we don’t have healthy detox processes, they accumulate and cause damage all over our bodies. Common triggers of impaired liver detoxification are:

Dietary triggers of impaired liver detoxification are many and significant, since you eat multiple times every day. This provides lots of opportunities to ingest something harmful.

High sugar and carbohydrate diet: When you eat excessive sugar and carbohydrates or refined foods, they need to be stored somewhere if you aren’t using them for energy. They end up stored in the body as fat and in the liver as glycogen.

Over time, if this process continues, the liver becomes inundated with fat, which compromises its function and promotes inflammation and insulin resistance, according to Dr. Mark Hyman.6

Processed foods: Any foods that come from a package may contain trans fats, preservatives, colorings, dyes, additives, and artificial sweeteners that are seen as toxins by your body. Additionally, some foods you think are safe may not be. Most cans are lined with BPA, rendering the foods inside very unhealthy.

Xenoestrogens: Xenoestrogens are substances that mimic the hormone estrogen. Foods and chemicals are sources of these compounds. Not only are they endocrine disruptors, but also toxins and carcinogens. Soy is the most common dietary source. Consumption of soy is linked to infertility, thyroid disruption, and breast and prostate cancers. Toxins produced in the processing of soy include nitrosamines, lysinoalanine, MSG, and aluminum.7

Water: Water can be one of the most toxic things we consume daily. Water can have microorganisms, chlorine, fluoride, agricultural and manufacturing runoff, pesticides, or heavy metals. Dr. Deanna Minish states, “Current estimates suggest that there are more than 2,000 toxins in tap water.”14 Bottled water is often not much better.

GMOs: Genetically modified foods contain genes that aren’t native to the original organism, and your body sees them as foreign and toxic. Corn, for instance, might contain Bt toxin or Roundup Ready genes so that it withstands pests better. These toxins degrade the stomach of the target insects and are now found to be harming humans, causing allergies and immune system activation similar to that of inflammatory conditions.8

Further, the pesticide Roundup (glyphosate) has been proven to have harmful mechanisms. According to Dr. Mercola, a recent study found that “glyphosate inhibits cytochrome P450 (CYP) enzymes, a large and diverse group of enzymes that catalyze the oxidation of organic substances.” This, the authors state, is “an overlooked component of its toxicity to mammals (which means humans).

By limiting the ability of these enzymes to detoxify foreign chemical compounds, glyphosate enhances the damaging effects of those chemicals and environmental toxins you may be exposed to.”9

Conventional meat and produce: Food grown or raised with conventional methods (non-organic) has some level of toxicity. Meat, poultry, and fish can be given antibiotics and drugs that affect their growth.

Vegetables and fruit can contain pesticides or be genetically engineered. One potent class, the organophosphates, are linked to infertility and impaired growth and development, and they’re known neurotoxins.

Nutrients: In order for detoxification to proceed the right way, it requires adequate amounts of the necessary raw materials to do so. These include amino acids, B vitamins, minerals, antioxidants, and sulfur-containing compounds. Deficiencies will result in impaired detox processes.

Dysbiosis

Dysbiosis occurs when there’s an imbalance between the beneficial and harmful organisms in your body, especially in the gut.

When this happens, the bad guys can produce toxins themselves or even undo all of the work the liver has done (deconjugation), allowing toxins back into circulation. While many organisms produce toxins (bacteria, mold, yeast, and parasites), here are some examples:

Candida: Yeast ferments sugars into ethanol and acetaldehyde, which are carcinogens that cause alcohol toxicity and hangovers. Candida increases levels of ammonia, which is another toxin.3 Yeast also produces toxins that allow them to bore into the intestinal wall, as some parasites and bacteria do.12

Clostridium difficile: Also known as C. diff, this bacteria produces several toxins that act on the gut and other cells of the body. These toxins are responsible for the awful diarrhea associated with an acute C. diff infection.

Mold: Molds are ubiquitous and often ingested in air and food. According to Dr. Jill Carnahan, “Some molds secrete mycotoxins. Exposure to mold and mold components is well known to trigger inflammation, allergies and asthma, oxidative stress, immune dysfunction, and neurological damage in humans.”13

Leaky Gut

Increased intestinal permeability, also known as leaky gut, occurs when the cells that line the intestinal tract become irritated and compromised, actually spreading apart and allowing particles that wouldn’t normally enter the bloodstream to pass through. This causes the immune system to react to these substances, producing inflammation.

Some of the irritants that cause leaky gut are toxins ingested in medications, alcohol, food, and water, as well as the byproducts of any allergic or sensitivity reaction. Further, dysbiosis and any gut infections compound this effect by the contribution of the toxins they produce.

When you have a leaky gut, your overall toxic burden is increased, because many more substances enter circulation than usual, and your liver has to detoxify all of them. This can place a significantly increased burden on the liver.

Toxins

Toxins are everywhere in our modern society. Unfortunately, our exposure to medications, supplements, chemicals, pesticides, pollutants, petrochemicals, heavy metals, tobacco smoke, and even alcohol are byproducts of contemporary living, and most of us have exceeded our liver’s natural capacity to cleanse us. If we can’t rid ourselves of these toxins, they accumulate and are stored in the body.

Heavy metals are everywhere—in the soil, in our homes and food, and as byproducts of industries, car exhaust, and tobacco smoke, so they’re hard to avoid. Things like lead, mercury, arsenic, cadmium, and aluminum are damaging toxins by themselves, but they also compromise our detoxification pathways, making matters worse.

Over 80,000 POPs have been released into the environment, and we lack information on how they affect human health. We know they’re particularly toxic, causing infertility and endocrine hormone disruption as well as being immunotoxic, neurotoxic, and carcinogenic.16 They’re also linked to cardiovascular disease, obesity, and diabetes.16

Even medications and supplements can have adverse effects on detoxification by damaging the liver. Certain prescription and over-the-counter drugs list liver damage as a side effect and a risk. Some of these include antidepressants, antipsychotics, corticosteroids, non-steroidal anti-inflammatory medications (NSAIDs) (particularly acetaminophen (Tylenol)), and others.3 Some herbal supplements are implicated here as well since they can be toxic to the liver if not used appropriately, such as kava kava, skullcap, and germander.

Stress

Not only do we have toxins that come from the outside, but we also generate them from within. Psychological stress, toxic relationships, illness, and anything else that disrupts your body’s natural balance produces biochemical changes that impair detoxification. But to fully understand toxicity, you must understand the concept of total load.

Dr. Mark Hyman explains this idea well. “This is a total amount of stressors on your system at any one time, and what happens is like a glass filling over with water. It takes a certain amount to fill the glass, and then, after a certain point, you put more in and it overflows. When our detoxification system is overwhelmed, is overloaded, that’s when we start getting symptoms and get sick, but it may take years of accumulated stress and toxins to get to that point.”18

He further points out that stress is a significant contributor to the total toxic load, including “the mental, emotional, and spiritual toxins that affect us; isolation, loneliness, anger, jealousy, and hostility, which all translate into toxins in our system.”18

Dr. Deanna Minich elaborates on that concept, stating, “When we don’t properly ‘eliminate’ unhealthy emotions, we may experience increased levels of stress. Stress not only causes inflammation, but can elicit poor digestive function. Those who experience chronic stress have a difficult time maintaining a positive outlook on life and are at greater risk for disease and premature death.”17

Chronic stressors cause an imbalance between the sympathetic (fight or flight) and parasympathetic (rest and digest) nervous systems, producing increased levels of the stress hormone cortisol. Over time, the constant cortisol elevation and demand leads to cortisol resistance and diminished cortisol.

Cortisol is the main anti-inflammatory hormone in your body, and when levels are low, inflammation increases. This results in oxidative stress and free radical damage. This in and of itself can damage the liver, but it also increases the toxic load the liver must clean up. Further, these changes can also perpetuate dysbiosis and leaky gut.

Symptoms of Impaired Liver Detoxification

The symptoms of impaired liver detoxification are system-wide in the body.

Liver function and organic acid testing is important so you know the state of your liver and detoxification pathways. When considering toxin testing, you need to be cautious, because some of the tests actually liberate toxins from storage in your cells, which can cause problems, especially if you have a leaky gut.

In general, it’s a good idea to make sure liver function has improved and the gut is healthy before testing and treating toxins.

General tests for liver function and blood sugar:

Total bilirubin

AST (aspartate aminotransferase)

ALT (alanine aminotransferase)

GGT (gamma glutamyl transpeptidase)

ALP (alkaline phosphatase)

Fasting insulin and glucose

CMP or comprehensive metabolic panel (will have most of the liver tests on it)

Supporting healthy and robust detoxification takes a little effort. Cleaning up your diet,environment, and lifestyle and adding in some supporting nutrients will lighten the load on your liver.

Detoxifying your diet is a good place to start, since we consume foods and liquids many times every single day.

Drink lots of water every day! Have at least eight glasses to flush your system. Add some liver for an added boost.

Eating organic and GMO-free will help you avoid many toxins.

Make sure your diet is rich in phytonutrients. Certain plants are known to support detoxification. The Brassica family, which includes broccoli, cabbage, cauliflower, and kale, contains the sulfuric compounds sulforaphane and indoles (I3C) that activate the Nrf2 gene, which increases many of the detoxification enzymes, especially in Phase 2.10,11,20 Garlic also has sulfur compounds that exert the same effect. Other Nrf2 activators include curcumin from turmeric, capsaicin from hot peppers, and resveratrol from grape skin or wine.11,20

Many leafy green herbs and plants support detoxification, including dandelion greens, cilantro, parsley, watercress, and chard. Use them in cooking, salads, smoothies, and juices.11,19

Artichoke, asparagus, and beets are healing to the liver with antioxidants that prevent liver damage. Artichoke is also one of the best stimulators of bile flow.11,19

Be sure to wash your produce well—even if it’s organic.

Cook with lower temperatures to avoid generating harmful chemicals. If you must grill, marinating with olive oil, lemon, and herbs such as rosemary, thyme, and oregano will help decrease the amount of HCAs and PAHs formed.

Avoid packaged foods as much as possible, including drinks in plastic bottles.

Invest in a water filter that filters out chlorine, fluoride, metals, and microbes. Most sink-mounted and pitcher systems don’t do this.

In addition to detox-supporting foods, there are nutrients obtained in supplements that directly support the liver and detoxification process.

Amino acids: This is one of the most critical nutrient groups, as these acids function in the detoxification process itself and serve as antioxidants.

N-acetylcysteine (NAC) is the precursor to glutathione, the master antioxidant of the body and a significant component of Phase 2 detoxification.

Cysteine and methionine contain sulfur and contribute to the sulfation pathways. Methionine is also a methyl donor to the methylation pathway in its activated form, S-adenosyl-methionine (SAMe). Glycine also performs conjugation down the glycination pathway.10,20

Glutathione: Taking glutathione itself as a supplement or through IV therapy is helpful when levels need to be increased.

B vitamins: The B complex vitamins, especially B5, B6, B12, and folic acid are significant co-factors in the Phase 1 and 2 detoxification reactions that help drive the reactions forward. The methylation pathway is also very dependent on sufficient levels of B12 and folic acid.

Minerals: Iron, magnesium, zinc, and selenium are all minerals that support the detoxification process as co-factors or through antioxidant functions.20

Antioxidants: Antioxidants such as alpha lipoic acid (ALA), vitamins A, C, and E, and flavonoids play an important role, since the detox process inherently produces free radicals that need to be quenched.10,11,20

Milk thistle: Silymarin is the polyphenol in milk thistle that promotes detoxification. The antioxidant capacity of silymarin can lower the liver’s oxidative stress associated with toxin metabolism, which has the effect of conserving cellular glutathione levels.11

Calcium-D-Glucarate: This nutrient helps prevent the deconjugation of toxins in the intestines by bacteria, thus preserving them for excretion.

Probiotics: Probiotics will help maintain the balance between good and bad bacteria in the gut, which supports healthy elimination and immune functions that in turn support the liver.

Diet and nutrients can support the detoxification process itself, but the other half of the equation involves cleaning up your world.

Lifestyle changes involve some work, since they require you to read labels, investigate your personal environment, and make some changes, but the benefits to your health are worth it.

Start reading labels: The more you know about what you put in, on, and around your body, the better. If you can’t pronounce it, you should probably avoid it. Knowledge allows you to make healthier choices for you and your family.

Clean up your products: Choose more natural personal care products, toiletries, baby products, home cleaners (especially window and bathroom cleaners), and lawn fertilizers. These products are laden with preservatives and chemicals. Baking soda, coconut oil, white vinegar, lemon, and essential oils can fill many of these roles without the unwanted toxins.

Detox your furniture and home: Furniture, paint, flooring (especially carpet), and building materials also contain chemicals that give off gas, meaning they constantly emit these toxic compounds into the air and you breath them in. Opt for more natural materials like bamboo, latex, wool, and organic cotton.

Get some houseplants: Many houseplants such as English ivy, rubber plants, peace lily, golden pothos, spider plants, Boston ferns, queen ferns, and dwarf date palms are all great at filtering toxins from the air.

Air filters: Having HEPA filtration added to your heating and cooling system will result in more toxins and fine particulates being removed from your home air.

Open your windows: Indoor air can be more toxic than outdoor air, so open your windows and let your home and office breathe.

Shower filter: Invest in a shower water filter or a whole house unit. Your skin is the largest organ in your body (and the liver is the largest organ inside) with a high capacity for absorption. It will absorb toxins in the water you bathe in.

De-stress: Lower your stress levels by finding ways to either decrease your stressors and create boundaries or find appropriate outlets like talking, journaling, or exercising. Getting out into nature can be especially helpful.

Toxic relationships: If you have a person in your life who’s causing you to feel bad, hurt, angry, or frustrated, you should let them know if you can. If you can’t, then try to limit contact with them.

Sleep: Getting 8-9 hours of sleep per night is important, since this is when your body regenerates and heals.

Sauna: Sweating is also a critical component of detoxification. You can do it through exercise or using a sauna. Saunas increase circulation and metabolic rate. Studies show that many metals, especially cadmium and nickel, are eliminated through sweat at higher levels than through urine.15

Bowel movements: Make sure you have 1-2 bowel movements per day. Daily elimination through the bowels, urine, and sweat are vital for proper detoxification.

Bacteria and your microbiome are an integral part of who you are—think of yourself as a bacterial hotel.

In fact, the bacteria living in and on your body outnumber your body cells by 10 times!

While there are 10 trillion cells in your body, there are 100 trillion bacteria that comprise an estimated 400-1,000 different species that coexist within you.2

The vast majority of them reside within your GI tract, weighing in at about 3-4 pounds.2,3,6

These bacteria have coexisted with us for millennia and are beneficial, helping us thrive by assisting in digesting and absorbing foods, producing vitamins and short-chain fatty acids, killing potential pathogens, maintaining a healthy weight, and supporting detoxification, inflammatory, immune, and hormone functions.6

The good bacteria and even a small amount of yeast are vital to your survival. Studies show that people with poor bacterial colonization after c-section birth and/or lack of breastfeeding have more health problems.3

While most of these organisms are helpful and essential, some are harmful and cause significant damage to the delicate balance of the ecosystem that exists in your gut.

What Exactly is Dysbiosis and How Does it Occur?

Dysbiosis occurs when harmful organisms, such as bacteria, fungi (yeast and mold), viruses, and parasites take over the gut environment and change your physiology such that it favors their survival (and that of other pathogens) to the detriment of your health.

What constitutes a healthy microbiome is constantly being redefined as more research is done. Recent research suggests that we may need to consider viruses, in addition to bacteria, as part of our commensal microbiome. “There have been suggestions that every individual harbors approximately 8-12 chronic viral infections at any given time, and these may be harmful only in the limited percentage of the population that has a certain genetic predisposition.”

The good bacteria collectively act as the Chief Operating Officer in your gut, keeping vital day-to-day functions occurring effortlessly without you even knowing it.

They help maintain immune and hormone function, modulate inflammation, protect you from pathogens, and metabolize and produce nutrients.

The primary reason this harmonious equilibrium of organisms can be maintained is that there’s a system of checks and balances so that one group can’t take control; however, when this balance is disrupted by stress, diet, medications, or toxins, dysbiosis is the result.

Dr. Leo Galland, M.D. simply states, “Dysbiosis is an unfavorable imbalance of the bacteria resulting in an intestinal flora that has harmful effects. The principal factors that regulate the composition and distribution of the GI flora are diet, motility, the nature of GI secretions, immune function, and the ingestion of antibiotic or probiotic substances.”8

Over time, the change in the intestinal ecosystem causes considerable chronic local and systemic effects. Dr. Gerard Mullin, M.D. asserts that, “Dysbiosis is not so much about the microbe as it’s about the effect of that microbe on a susceptible host; it’s about the relationship between the host and the microbe.”14

For example, people with inflammatory or autoimmune conditions often present with a pathogenic inflammatory response to a non-inflammatory microbe due to the activation of the immune system and the inflammatory chemicals produced in that interaction.12

If it’s caught and reversed quickly, you may not have too many ill effects. However, if this condition is allowed to progress, it can lead to serious health problems ranging from gas, diarrhea, constipation, and acne to joint pain, chronic fatigue, and autoimmunity.

Further, intestinal dysbiosis can lead to dysbiosis of other mucosal areas such as the mouth, nose, lungs, skin, eyes, and vaginal and urinary tracts, making you more vulnerable to other infections.

Triggers of Dysbiosis

Triggers for the development of dysbiosis are usually multiple and cumulative—meaning that the more you experience these as a part of your lifestyle, the more likely you are not only to have dysbiosis but also to have many of the symptoms associated with it. The main primary contributors to dysbiosis are:

Poor bacterial colonization

Medications

Stress

Diet

Environmental toxins

Infections

Trigger of Dysbiosis: Poor Colonization

The first step toward dysbiosis can actually occur during your birth. The process of vaginal birth naturally initiates the critical event of bacterial colonization.

Infants born this way have a microbiota that reflects their mother’s fecal and vaginal flora, where those born via cesarean section have a flora reflective of the hospital environment and the health care workers.3,12

Children born through c-section are also at risk of delayed access to breast milk, which can be an additional detriment to the development of a healthy flora.3

Research by Giacomo Biasucci et al. in the September 2008 issue of the Journal of Nutrition showed that the gut microbiota after c-section was characterized by a lack of Bifidobacteria species, which are thought to be important to the postnatal development of the immune system, whereas vaginally delivered neonates showed a predominance of these species.3,12

It’s also important that women who want to conceive are aware of the health of their intestinal flora, as infants born to women with dysbiosis also have dysbiosis. Taking care of GI infections and imbalances, as well as supplementing with specific probiotics, will help impart a healthy flora to the baby.

Trigger of Dysbiosis: Medications

Several categories of medications can directly impact the health of the GI flora. The most significant ones include:

Antibiotics: This class of medications is the most common and significant cause of major alterations in normal GI tract flora.6

Depending upon the scope of antimicrobial activity, antibiotics can wipe out multiple categories of beneficial organisms, leading to dysbiosis—the antibiotics don’t differentiate between the good guys and bad guys

PPIs: Proton pump inhibitors that block stomach acid (HCl) production provide a gateway for dysbiosis to develop, as HCl is critical to the normal process of digestion and acts as defense against pathogens. PPIs are known to directly alter the gut flora as well.

NSAIDs: Chronic use of nonsteroidal anti-inflammatory drugs such as ibuprofen, naproxen sodium, aspirin, and indomethacin can inhibit the growth of good bacteria and alter the gut flora, resulting in leaky gut, which further perpetuates dysbiosis.

Hormone-Based Medications: According to Gut and Psychology Syndrome author Dr. Natasha Campbell- McBride, M.D., “The use of birth control pills and immune system-altering steroidal hormones change the gut flora by harming the beneficial bacteria.” Widespread use of hormone-based medication isn’t often mentioned yet is a significant contributor to dysbiosis.

Trigger of Dysbiosis: Stress

Stress is one of the most important triggers of dysbiosis, as it’s something most of us have plenty of in our lives, and we don’t do much to counterbalance its effects.

Further, chronic stress diminishes immunity by depleting the antibody secretory IgA (sIgA), as well as essential hormones, and promotes inflammation, which can all result in a leaky gut.6,14

The catecholamine hormones (adrenaline and noradrenaline) stimulate growth of gram-negative organisms such as E.coli, Yersinia, and Pseudomonas, which promote inflammation and immune system activation by producing the endotoxin LPS (lipopolysaccharide).3,6,14

Many of these gram-negative bacteria are normal inhabitants of the large intestine; however, when the good flora are diminished, they can’t keep growth of these opportunistic organisms in check. This leads to dysbiosis and inflammation.

All of this culminates in a vicious, self-perpetuating cycle when you’re chronically stressed.

Trigger of Dysbiosis: Diet

Diet, along with stress, exerts the most impact on the balance and health of the gut flora.

Sulfates: Consumption of foods high in sulfates promotes the growth of bacteria that produce a toxic gas called hydrogen sulfide (think stinky egg smell), which results in depletion of colonic nutrients and leaky gut. Foods high in sulfates include eggs, cruciferous vegetables, dairy, dried fruit, alcohol, meat, baked goods, and processed foods.6

High Protein: Excessive consumption of protein, especially in the presence of enzyme deficiency, allows bacteria to ferment the undigested protein particles and produce toxic metabolites such as ammonia, indoles, phenols, and sulfides, which are carcinogenic and promote migraines and mood disorders.6,7 High protein diets can also promote inflammation and hormone imbalance through the action of some bacterial enzymes such as beta-glucuronidase.6,7

High Sugar and Carbohydrates: Diets high in sugars and simple carbohydrates are characterized by increased bacterial fermentation and decreased intestinal transit speed, allowing for toxic metabolites to sit in the intestines longer and potentiate inflammation.6,7

Bad Fats: Eating a diet high in trans fats and certain chemically processed or genetically modified fats inhibits the growth of protective bacteria.7 These fats include any trans fat labeled “partially hydrogenated,” shortening and margarine, as well as oils including canola, corn, soybean, peanut, sunflower, and safflower.

Processed Foods: Preservatives, dyes, emulsifiers, surfactants, additives, and flavoring all negatively impact the health of the gut flora, as they’re toxins. When you read a label, generally if you can’t pronounce it or don’t know what it is, you shouldn’t eat it.

Food sensitivities and allergies represent a potent trigger for dysbiosis, as the immune system reacts to the protein peptides of the offending foods by producing pro-inflammatory chemicals called cytokines that damage the intestinal mucosa, not only leading to a leaky gut but also making the environment inhospitable to the good flora.

In conditions such as Celiac, where the immune system is reacting to the family of gluten-related peptides, it’s been discovered that the gut microbiota plays a significant role in the development and progression of the illness.

Research has found that levels of beneficial flora such as Lactobacillus and Bifidobacteria in Celiac patients is much lower than in healthy individuals.7

Overall, higher incidence of gram-negative and pro-inflammatory bacteria present in the microbiota is linked to the symptoms associated with the disease by favoring the pathological progress of the disorder.7

Studies have also noted that a similar profile of decreased good bacteria and higher levels of bad bacteria are seen in the development of food sensitivities and allergies to milk, eggs, and nuts.7

It’s important to note that you can develop a food sensitivity or allergy at any time in your life to any food, not just the common ones (gluten, dairy, soy, corn, eggs, shellfish, and nuts).

GMO (genetically modified organism) or hybridized foods also represent a potent source for dysbiosis and the development of food sensitivities, as they aren’t as recognizable to your immune system as the original food form. This can trigger an inflammatory and immune response in the gut, potentiating dysbiosis.

Trigger of Dysbiosis: Environmental Toxins

Environmental toxins are everywhere—metals, volatile organic compounds (VOCs), and chemicals are found in the air, water, soil, industry, and products used on your body and in the home.

Food can also be a significant source of toxins depending upon where and how it’s grown, as well as if it’s processed.

If you’re a fan of grilling your food, you are adding yet another layer of toxins from the heterocyclic amines (HCAs) that are produced in the tasty charred portions. The cumulative effect of exposure to these substances over time can have a profound impact on the health of your intestinal microbiome, potentially leading to dysbiosis.

A 2008 study found that the volatile derivatives from metals such as mercury, arsenic, bismuth, and antimony exert their toxic effects on human health not only by direct interaction with host cells but also by disturbing the physiological gut microflora.18

The metals not only alter the composition of the organisms in the gut, but the bacteria themselves can transform the toxic metals into even more toxic compounds. Toxins of all kinds shift the balance of the flora into supporting the harmful organisms over the favorable ones.

Trigger of Dysbiosis: Infections

Toxins are not only acquired from the external environment but can also be prevalent internally, because they’re produced from infectious organisms such as certain bacteria, mold, yeast, viruses, and parasites. These organisms contribute to dysbiosis because they produce toxins that are detrimental to your body by:

Altering normal GI function: The organisms exert their damaging effects by decreasing gut motility, decreasing the amount of stomach acid and digestive enzymes, and altering bile production. These mechanisms help ensure their survival.16

Promoting inflammation: GI infections promote inflammation through the production of toxins such as lipopolysaccharides (LPS) in certain gram-negative bacteria and mycotoxins from mold. They also generate several different types of immune responses, which promote inflammation and also produce autoimmunity.16

Altering the GI flora: The gut microflora is often already compromised to some extent when a GI infection occurs. The infective organisms increase dysbiosis by their mere presence and by making the intestinal environment more hospitable to other pathogens and opportunistic commensal organisms (organisms that are normally found in the intestines of healthy individuals that take advantage of your compromised physiology).

After infectious organisms take hold, you may experience gas, bloating, diarrhea, constipation, or even no gut-related symptoms at all.

Brain fog, fatigue, sleeplessness, joint pain, depressed mood, and anxiety are often related to these infections. Some of the most common organisms include:

SIBO: Small intestinal bacterial overgrowth occurs when organisms from the colon inhabit the small intestine, where fewer bacteria reside.

Escherichia coli, Streptococcus, Staphylococcus, and Klebsiella are species frequently associated with SIBO. SIBO is complex, because the constituent organisms vary widely from person to person, as do symptoms, which can include constipation, diarrhea, gas, bloating, belching, stomach pain, malabsorption, brain fog, mood disorders, headaches, fatigue, and rashes, among others.

H. pylori: Helicobacter pylori is a spiral-shaped bacteria that is estimated to inhabit two-thirds of the world’s population. Some people happily coexist with it while others develop chronic conditions, because it can become opportunistic.

It alters immune function and stomach acid production to aid its survival while you experience reflux, indigestion, gas, bloating, and stomach pain.

Candida: Candida (yeast) is a fungus that lives in your mouth and intestines to aid with digestion and nutrient absorption.19 It can become pathogenic and rapidly increase in numbers if your immune system is compromised from stress or illness.

The infection can be almost anywhere in your body, from the mouth and stomach to the urinary tract, skin, and lungs. Some symptoms associated with Candida include sugar cravings, depression, anxiety, gas, bloating, headaches, rashes, and skin discoloration.

While the previously-mentioned infections are commonly related to dysbiosis, some important and often overlooked sources of infection include:

Mold: Mold is a fungus like Candida, and both are ubiquitous. Some common types of mold associated with dysbiosis include Aspergillus, Penicillium, Stachybotrys, and Alternaria.

The toxins produced from mold can be very harmful to the good gut bacteria and the host (you). These toxins produce symptoms ranging from mild to severe fatigue, sore throats, nosebleeds, headaches, diarrhea, brain fog, food sensitivities, and memory loss.

Tick-borne Illness: Tick-borne illnesses are prevalent primary infections or co-infections that can result in dysbiosis through several mechanisms.

First-line treatment of these infections often involves the use of antibiotics for weeks in acute cases and for months for chronic infections, killing off the good bacteria and promoting yeast overgrowth according to Dr. Leo Galland.21

These infections also result in “Bell’s Palsy of the gut,” ranging from paralysis of the gut to decreased GI motility, allowing dysbiosis to occur. 21,22

Lyme disease, an infection acquired through the bite of a tick infected with the bacteria Borrelia burgdorferi, is the most commonly-known infection. Babesia, Rickettsia (Rocky Mountain Spotted Fever), Ehrlichia, and Bartonella are also frequently identified as infectious bacteria from tick bites. Symptoms include rash, fatigue (often chronic), fever, aches, stiffness, brain fog, and constipation.

Viruses: Chronic viral infection is a common but often ignored cause of dysbiosis. Enteric (GI) viruses play an important role in the microflora of the gut, as they’re present in all of us and affect not only our gene expression but also the composition of the gut microbiota.

A 2014 study notes, “Viruses may act directly on the host epithelium and immune system to induce inflammation, or may alter luminal bacterial composition that then provokes disease.” 23

A further complication is that some viruses such as cytomegalovirus (CMV) and Epstein-Barr virus can remain latent after initial infection and only become active again under stress or immunosuppression, producing inflammation and GI symptoms that don’t appear to be related to the current pathological process.23

Symptoms and Effects of Dysbiosis

Alteration of the gut microbiome can have wide-ranging consequences on a person systemically—these effects aren’t limited to the gut.

The inflammatory process generated by dysbiosis is one of the primary root causes in many conditions.

The inflammation produces chemical changes in the body that activate the immune system, and it also increases or decreases the expression of certain genes, enabling the disease process to evolve.

What began as smoldering embers becomes a systemic wildfire when there’s no intervention or lifestyle change, allowing a simple process to potentially become a complex condition that is difficult to manage.

Treatment of dysbiosis can be as basic as using probiotics and gut-supporting nutrients in the most simple cases, or it can escalate to treating multiple infections and addressing autoimmunity in more complex cases.

Identifying and resolving all triggers and making appropriate lifelong lifestyle changes are key to reversing dysbiosis and eliminating inflammation.

The process of addressing triggers should begin with identification and elimination of all potential pathogenic GI infections through testing. Non-pathogenic bacterial overgrowth must also be identified and treated. This should be the first step of a comprehensive 5R program that includes these components:

1. Remove sources of irritation and inflammation:

Remove all sources of parasitic, fungal, and bacterial infections in the gut (from mouth to anus). If you take care of these without resolution of symptoms, look into viruses, mold, and other infections like tick-borne illnesses. Infections of the jaw from root canals and dental work are sometimes a source of hidden infection that should be investigated as well.

Try to eliminate the use of medications known to contribute to dysbiosis and irritation of the intestinal lining.

Refrain from alcohol consumption, as you’re trying to restore bacterial balance in the gut.

Reduce toxin exposure by eating organic when possible, using cleaner personal care and home products, and filtering your home air and water. Many green plants provide natural toxin filtration.

Prepare foods so that there are no charred areas produced. Marinating foods with lemon, garlic, and rosemary for several hours before cooking will help buffer the effects of any char that is produced.

2. Replace the nutrients your body needs to heal:

Beginning a meal with digestive enzymes and betaine hydrochloride will allow for proper breakdown and absorption of nutrients.

Prebiotic fiber such as FOS and inulin from onions, garlic, blueberries, asparagus, bananas, chicory, and artichoke promote the growth of beneficial bacteria and discourage harmful ones. Since these fibers are non-digestible by humans, the good flora can use them as a nutrient source. They also help prevent constipation and diarrhea by maintaining colonic balance.12

Fermented foods such as yogurt, kefir, kombucha, sauerkraut, kimchi, and some varieties of pickled vegetables are cultured with bacteria and yeast strains that help maintain intestinal flora.

Resistant starches, or starches that resist digestion until they reach the colon, can be found in raw potatoes, green bananas, green plantains, parboiled rice, lightly-cooked and cooled potatoes, or legumes (that have been soaked and sprouted). Once the resistant starches reach the colon, the bacteria digest or ferment them, producing short-chain fatty acids (SCFAs) that support bacteria and intestinal cell health and modulate inflammation. Added benefits are that they help improve insulin sensitivity, as well as blood sugar and body composition.

Soluble (completely fermentable) and insoluble fibers (little to no fermentation) like grains, fruits, vegetables, and psyllium also provide nutrients to the beneficial bacteria and help prevent constipation.12 They keep your bowels moving.

3. Re-inoculate with good bacteria to restore the flora:

Using a high-qualityprobiotic with at least 50 billion CFU twice daily will help restore the gut flora. Lactobacillus and Bifidobacter species are best in most cases; however, there are other beneficial strains that can be used. Start off using them slowly and work up to the recommended doses.

Fermented foods such as sauerkraut, kimchi, and kombucha, as well as kefir and yogurt (you can use dairy or non-dairy based), contain live, active cultures that will help the good bacteria stick around.

Dysbiosis often involves leaky gut as well as disruption of normal physiological processes of digestion, which all need to be addressed in order to maintain a healthy flora and GI function. This includes using betaine HCl to increase stomach acid, digestive enzymes to assist the pancreas, intestines, and liver until they produce adequate levels on their own, and sometimes ox bile to assist the liver in the digestion of fats.

Additionally, motility—the ability to keep waste and toxins moving through the GI tract—often needs to be repaired and restored. Ginger and d-limonene are good agents to stimulate GI motility. Exercise or movement and proper hydration are also great ways to keep the bowels moving.

Calming the nervous system and decreasing stress through breathing techniques, meditation, yoga, Tai Chi, or walks in nature are great ways to achieve this. Stress for most people is unavoidable, so learning to manage it through creating boundaries, learning to say no, or having a proper outlet to release it is key.

Exercise and movement are also essential in decreasing stress and maintaining the balance of the body and the brain.

One of the most important measures you can take is to fall asleep at a reasonable hour (10 pm is ideal), as well as get at least eight hours ofhigh quality, uninterrupted sleep. Sleep is crucial to the healing process, as well as the maintenance of overall good health.